Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwate
- PDF / 1,357,630 Bytes
- 16 Pages / 595.276 x 790.866 pts Page_size
- 104 Downloads / 170 Views
RESEARCH ARTICLE
Environmental Microbiome
Open Access
Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond Jessica Chopyk1,2* , Daniel J. Nasko3, Sarah Allard1, Anthony Bui1, Mihai Pop3, Emmanuel F. Mongodin4 and Amy R. Sapkota1
Abstract Background: Ponds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, highthroughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial and viral communities in a freshwater agricultural pond. Results: Water samples (n = 14) were collected from a Mid-Atlantic agricultural pond between June 2017 and May 2018 and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, pooled, and subjected to 16S rRNA gene and shotgun sequencing on the Illumina HiSeq 2500 platform. Additionally, on eight occasions water filtrates were processed for viral metagenomes (viromes) using chemical concentration and then shotgun sequenced. A ubiquitous freshwater phylum, Proteobacteria was abundant at all sampling dates throughout the year. However, environmental characteristics appeared to drive the structure of the community. For instance, the abundance of Cyanobacteria (e.g. Nostoc) increased with rising water temperatures, while a storm event appeared to trigger an increase in overall bacterial diversity, as well as the relative abundance of Bacteroidetes. This event was also associated with an increase in the number of antibiotic resistance genes. The viral fractions were dominated by dsDNA of the order Caudovirales, namely Siphoviridae and Myovirdae. Conclusions: Overall, this study provides one of the largest datasets on pond water microbial ecology to date, revealing seasonal trends in the microbial taxonomic composition and functional potential. Keywords: Metagenome, Shotgun, Agricultural irrigation, Antibiotic resistance, Microbial communities, Bacteria, Bacteriophage
* Correspondence: [email protected] 1 Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, USA 2 Department of Pathology University of California San Diego, La Jolla, California, USA Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicat
Data Loading...
